Pole position was just reward for Italian Bezzecchi who has been fastest all weekend in practice sessions as he looks to move back into second place in the championship standings after Pramac Racing's Jorge Martin leapfrogged him in Germany.
With a time of 1:31.472, Bezzecchi also became the 13th different polesitter at Assen in 13 visits to the Cathedral of Speed as Ducati bikes continued their dominance this season with a front-row lockout.
Japanese manufacturer Yamaha have struggled this season but Fabio Quartararo finished a creditable fourth and will be joined on the second row by Red Bull KTM's Brad Binder and Aprilia's Aleix Espargaro.
Honda's troubles followed them to Assen as Marc Marquez collided with the back of Ducati's Enea Bastianini in Q1, bringing out the yellow flags.
Marquez, who has yet to finish a race this season, will start 17th on the grid as a result.